detection of aberrant rna transcripts

[golharam]

Hi all - I have some RNA-Seq data in which I'm trying to track down any transcripts that might have been rendered non-functional by a mutation. I'm expecting a novel splice variant or a mutation somewhere that would have led to a missense codon or early stop codon or something like that. I'm currently running that data through tophat/cufflinks.

I haven't seen much in the literature, but I could also not be searching correctly. It seems everyone is concerned about expression levels. What there any recommended tools that will detect the type of mutations I'm referring to?